Most CCDs extract color information using a Bayer Filter[1] over them. Each square is a pixel in the megapixel count (a 1 megapixel sensor would have 250k red, 250k blue and 500k green photo sites). Algorithms are used to get RGB values for each pixel in that setup (luminance is extracted from the green sites). However, all the algorithms for the Bayer filter have a tendency to generate Moiré patterns[2]. To combat that, most sensors have anti-alias filters in front of them. This reduces the size of detail that can resolved by a sensor, but it also prevents some of the ugly consequences of the Bayer filter.

Some companies have experimented with other sensors or other patterns. The new Fuji X-PRO1 is using a non-Bayer filter, which should be interesting if it works well (it also does not have an anti-alias filter). There are also Foveon sensors, which use the selective permeability of silicon to different kinds of light instead of a pattern of photo sites.[3]

[1] http://en.wikipedia.org/wiki/Bayer_filter [2] http://en.wikipedia.org/wiki/Moir%C3%A9_pattern [3] http://en.wikipedia.org/wiki/Foveon_X3_sensor